Glad that helped. Making it easily accessible to students means doing most of
the work for them. In the case of Jmol that means setting up buttons or
checkboxes or whatever user interface then scripting what you want the students
to see. In the case of viewing the MOs or some other surface you could create
a button which the students would click to show the surface. Would be easy
enough to include in that script a command to return to model 1 so the MOs
would be available to view.
Those surfaces in Spartan are basically the electron density surface colored
according to other properties. Jmol will certainly allow you to visualize the
electron density surface. My understanding is that you can also color it by
whatever property you want. There would be some serious scripting involved in
doing this. Without knowing exactly what is in the smol file, I would imagine
the data for those properties are there somewhere. you would have to grab that
data somehow then instruct Jmol to use it as the basis for coloring the
surface. I'm no expert on this, but perhaps someone else can help with the
details of this.
***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***********************************************
On Jun 30, 2010, at 2:09 PM, Pshemak Maslak wrote:
> On 6/30/2010 10:38 AM, Jeff Hansen wrote:
>>
>> OK. So ignore my previous post. I was thinking you wanted to view the
>> vibrations and MOs simultaneously. Obviously not what you want. You said
>> that "MO #" gives a message that no MO coefficient data is available. This
>> would be true unless you are in model 1. I think just stopping vibrations
>> will leave you in whichever model was showing when you stopped vibrations.
>> Unless that happened to be the first model then you wouldn't have any MOs
>> available. Switch to model 1 and the MOs should be available.
>>
>> What other surfaces are you interested in?
> Thanks. I think your comments helped me to figure out how that works. There
> is no bug: it is how it is designed: one has to (manually i.e. through menu
> or script) return back to the frame with MO info.
> As you have said stopping vibration does not automatically return Jmol to
> frame (model) 1 (where MO's are).
>
> I am mostly interested in setting Jmol in such a way that is easily
> accesiblke to students. I do not want the Jmol "mechanics" to divert from the
> chemistry contents.
>
> Since Spartan easily calculates various surfaces (density(bonds),
> density(HOMO) or density(LUMO to name the few, I was wandering if they are
> written into smol files and whether they are accessible through Jmol.
>
> Thanks!
>
> PM.
>
>
>
>
>>
>>
>> ***********************************************
>> Jeff Hansen
>> Department of Chemistry and Biochemistry
>> DePauw University
>> 602 S. College Ave.
>> Greencastle, IN 46135
>> jhan...@depauw.edu
>> ***********************************************
>>
>>
>> On Jun 30, 2010, at 10:27 AM, Pshemak Maslak wrote:
>>
>>> On 6/30/2010 9:32 AM, Robert Hanson wrote:
>>>>
>>>> When Jmol reads a Spartan smol file, it accesses all vibrations and all
>>>> molecular orbitals (supposedly!) They should be accessible via the
>>>> right-click menu (or by clicking the "Jmol" logo"). MOs are under
>>>> "surfaces"; vibrations are under "model" (at the top).
>>> Thanks. I am new to Jmol, but not that new. :-) I have no problems
>>> individually visualizing any of the vibrations, or MOs, or mep surfaces
>>> from smol files..
>>>
>>> The problem (possibly a bug as you have suggested) is that once vibrations
>>> are visualized the MOs or mep are no longer accessible without reloading
>>> the smol file. I am guessing that the "frame" that holds MO and mep data
>>> is not longer read by Jmol after one of the vibrational frames was read.
>>> For example, after stopping vibrations (vibration off) "MO #" would give a
>>> message that no MO coefficient data is available for this frame, and no MO
>>> is displayed. When I choose all vibrational frames (from the menu) I get
>>> the same error message, but the MO loads!
>>>
>>>>
>>>> Each vibration is another "frame" or "model", and generally one of those
>>>> models has the MOs. For some readers that is the first model, some the
>>>> second, some the last. It all depends upon the reader. With Spartan, the
>>>> MOs should be in model 1, and the vibrations should be the models after
>>>> that.
>>>>
>>>> Makes sure you have issued
>>>>
>>>> vibration on
>>>>
>>>> if you want to see the vibrations or using that menu, Vibration->ON
>>>>
>>>> http://chemapps.stolaf.edu/jmol/docs/examples-11/data/C6H6.smol should be
>>>> a good example of this.
>>>>
>>>> Bob
>>> Coming back to my related questions:
>>>
>>> Can any other surfaces (in addition to MOs and mep) be visualized through
>>> smol files?
>>>
>>> Can Jmol write jvxl files with multiple surfaces (for example selected MOs)?
>>>
>>> Thanks for all your help.
>>>
>>> PM
>>>
>>>>
>>>> On Wed, Jun 30, 2010 at 6:19 AM, Pshemak Maslak <p...@chem.psu.edu> wrote:
>>>> On 6/29/2010 7:20 PM, Robert Hanson wrote:
>>>>>
>>>>> I'll look into the mep/mo business. Should not be a problem. Just a bug,
>>>>> I think.
>>>> Thank you very much for your help.
>>>>
>>>> I do have two related questions:
>>>>
>>>> 1. Can more than one surface be read from these files by Jmol?
>>>>
>>>> 2. Can Jmol write jvxl files with multiple surfaces?
>>>>
>>>>
>>>> Since I have just started learning Jmol and have noticed the incredible
>>>> amount of work you have put into this project, I would like to take
>>>> this opportunity to express my thanks for your contribution to the
>>>> development of such an invaluable tool for organic chemists.
>>>>
>>>> PM
>>>>
>>>>
>>>>
>>>>>
>>>>> On Mon, Jun 28, 2010 at 7:45 AM, Pshemak Maslak <p...@chem.psu.edu> wrote:
>>>>> On 6/25/2010 4:51 PM, Greeves, Nick wrote:
>>>>> > I have used smol files for vibration
>>>>> > e.g. http://www.chemtube3d.com/vibrationsC2H4.htm and they work well
>>>>> > without any server side settings.
>>>>> >
>>>>> > All the best
>>>>> > Nick
>>>>> > Sent from my iPad
>>>>> Thank you very much for the example. Your case indeed clarifies the
>>>>> behavior: vibration and surfaces (mep and MOs) appear to be mutually
>>>>> exclusive with
>>>>> smol files, and if you do not reload, you cannot access the surfaces.
>>>>>
>>>>> Try the following: start any of the vibrations. Now stop it (check the
>>>>> vibration check box twice). Now check if MO's are still in the menu and
>>>>> what kind mep loads (not the one form smol, but one generated by Jmol).
>>>>>
>>>>> This is exactly what I was trying to explain (I am new to Jmol).
>>>>>
>>>>> That issue was not related to the MIME type question (although both were
>>>>> about smol). The same happens on the desktop Jmol.
>>>>>
>>>>> Thank you for your assistance.
>>>>>
>>>>> PM
>>>>>
>>>>>
>>>>>
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>>>>>
>>>>> --
>>>>> Robert M. Hanson
>>>>> Professor of Chemistry
>>>>> St. Olaf College
>>>>> 1520 St. Olaf Ave.
>>>>> Northfield, MN 55057
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>>>>>
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>>>>> it is better to take what answer we get.
>>>>>
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>>>>
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>>>>
>>>>
>>>> --
>>>> Robert M. Hanson
>>>> Professor of Chemistry
>>>> St. Olaf College
>>>> 1520 St. Olaf Ave.
>>>> Northfield, MN 55057
>>>> http://www.stolaf.edu/people/hansonr
>>>> phone: 507-786-3107
>>>>
>>>>
>>>> If nature does not answer first what we want,
>>>> it is better to take what answer we get.
>>>>
>>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>>>
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